Learning node labels with multi-category Hopfield networks

In several real-world node label prediction problems on graphs, in fields ranging from computational biology to World Wide Web analysis, nodes can be partitioned into categories different from the classes to be predicted, on the basis of their characteristics or their common properties. Such partitions may provide further information about node classification that classical machine learning algorithms do not take into account. We introduce a novel family of parametric Hopfield networks (m-category Hopfield networks) and a novel algorithm (Hopfield multi-category \u2014 HoMCat ), designed to appropriately exploit the presence of property-based partitions of nodes into multiple categories. Moreover, the proposed model adopts a cost-sensitive learning strategy to prevent the remarkable decay in performance usually observed when instance labels are unbalanced, that is, when one class of labels is highly underrepresented than the other one. We validate the proposed model on both synthetic and real-world data, in the context of multi-species function prediction, where the classes to be predicted are the Gene Ontology terms and the categories the different species in the multi-species protein network. We carried out an intensive experimental validation, which on the one hand compares HoMCat with several state-of-the-art graph-based algorithms, and on the other hand reveals that exploiting meaningful prior partitions of input data can substantially improve classification performances

Influence of age, reproductive cycling status, and menstruation on the vaginal microbiome in baboons (Papio anubis)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111197/1/ajp22378.pd

Strategies to build a positive and inclusive Antarctic field work environment

Support from National Science Foundation (NSF: Grants 1738913, 1738896, 1738942, 1738992, 1738896, 1738934) and Natural Environment Research Council (NERC: Grants NE/S006788/1, NE/S006605/1, NE/S00677X/1). This research was supported in part by the NOAA cooperative agreement NA17OAR4320101. Logistics provided by NSF-U.S. Antarctic Program and NERC-British Antarctic Survey. ITGC Contribution No. ITGC-084.To increase inclusivity, diversity, equity and accessibility in Antarctic science, we must build more positive and inclusive Antarctic field work environments. The International Thwaites Glacier Collaboration (ITGC) has engaged in efforts to contribute to that goal through a variety of activities since 2018, including creating an open-access 'Field and Ship Best Practices' guide, engaging in pre-field season team dynamics meetings, and surveying post-field season reflections and experiences. We report specific actions taken by ITGC and their outcomes. We found that strong and supported early career researchers brought new and important perspectives regarding strategies for transforming culture. We discovered that engaged and involved senior leadership was also critical for expanding participation and securing funding to support efforts. Pre-field discussions involving all field team members were particularly helpful for setting expectations, improving sense of belonging, describing field work best practices, and co-creating a positive work culture.Publisher PDFPeer reviewe

Bacteria isolated from lung modulate asthma susceptibility in mice

Asthma is a chronic, non-curable, multifactorial disease with increasing incidence in industrial countries. This study evaluates the direct contribution of lung microbial components in allergic asthma in mice. Germ-Free and Specific-Pathogen-Free mice display similar susceptibilities to House Dust Mice-induced allergic asthma, indicating that the absence of bacteria confers no protection or increased risk to aeroallergens. In early life, allergic asthma changes the pattern of lung microbiota, and lung bacteria reciprocally modulate aeroallergen responsiveness. Primo-colonizing cultivable strains were screened for their immunoregulatory properties following their isolation from neonatal lungs. Intranasal inoculation of lung bacteria influenced the outcome of allergic asthma development: the strain CNCM I 4970 exacerbated some asthma features whereas the pro-Th1 strain CNCM I 4969 had protective effects. Thus, we confirm that appropriate bacterial lung stimuli during early life are critical for susceptibility to allergic asthma in young adults

Comparing microbiotas in the upper aerodigestive and lower respiratory tracts of lambs

Abstract Background Recently, the importance of the lung microbiota during health and disease has been examined in humans and in small animal models. Whilst sheep have been proposed as an appropriate large animal model for studying the pathophysiology of a number of important human respiratory diseases, it is clearly important to continually define the limits of agreement between these systems as new concepts emerge. In humans, it has recently been established that the lung microbiota is seeded by microbes from the oral cavity. We sought to determine whether the same was true in sheep. Results We took lung fluid and upper aerodigestive tract (oropharyngeal) swab samples from 40 lambs (7 weeks old). DNA extraction was performed, and the V2-V3 region of the 16S rRNA gene was amplified by PCR then sequenced via Illumina Miseq. Oropharyngeal swabs were either dominated by bacteria commonly associated with the rumen or by bacteria commonly associated with the upper aerodigestive tract. Lung microbiota samples did not resemble either the upper aerodigestive tract samples or reagent-only controls. Some rumen-associated bacteria were found in lung fluids, indicating that inhalation of ruminal bacteria does occur. We also identified several bacteria which were significantly more abundant in lung fluids than in the upper aerodigestive tract swabs, the most predominant of which was classified as Staphylococcus equorum. Conclusions In contrast to humans, we found that the lung microbiota of lambs is dissimilar to that of the upper aerodigestive tract, and we suggest that this may be related to physiological and anatomical differences between sheep and humans. Understanding the comparative physiology and anatomy underlying differences in lung microbiota between species will provide a foundation upon which to interpret changes associated with disease and/or environment

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

Background: Many patients with COVID-19 have been treated with plasma containing anti-SARS-CoV-2 antibodies. We aimed to evaluate the safety and efficacy of convalescent plasma therapy in patients admitted to hospital with COVID-19. Methods: This randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing several possible treatments in patients hospitalised with COVID-19 in the UK. The trial is underway at 177 NHS hospitals from across the UK. Eligible and consenting patients were randomly assigned (1:1) to receive either usual care alone (usual care group) or usual care plus high-titre convalescent plasma (convalescent plasma group). The primary outcome was 28-day mortality, analysed on an intention-to-treat basis. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936. Findings: Between May 28, 2020, and Jan 15, 2021, 11558 (71%) of 16287 patients enrolled in RECOVERY were eligible to receive convalescent plasma and were assigned to either the convalescent plasma group or the usual care group. There was no significant difference in 28-day mortality between the two groups: 1399 (24%) of 5795 patients in the convalescent plasma group and 1408 (24%) of 5763 patients in the usual care group died within 28 days (rate ratio 1·00, 95% CI 0·93–1·07; p=0·95). The 28-day mortality rate ratio was similar in all prespecified subgroups of patients, including in those patients without detectable SARS-CoV-2 antibodies at randomisation. Allocation to convalescent plasma had no significant effect on the proportion of patients discharged from hospital within 28 days (3832 [66%] patients in the convalescent plasma group vs 3822 [66%] patients in the usual care group; rate ratio 0·99, 95% CI 0·94–1·03; p=0·57). Among those not on invasive mechanical ventilation at randomisation, there was no significant difference in the proportion of patients meeting the composite endpoint of progression to invasive mechanical ventilation or death (1568 [29%] of 5493 patients in the convalescent plasma group vs 1568 [29%] of 5448 patients in the usual care group; rate ratio 0·99, 95% CI 0·93–1·05; p=0·79). Interpretation: In patients hospitalised with COVID-19, high-titre convalescent plasma did not improve survival or other prespecified clinical outcomes. Funding: UK Research and Innovation (Medical Research Council) and National Institute of Health Research